[BioC] Restore lost mm probes in an altcdfenv?

[Mike Mahowald]

Hi all,
     Being an R novice I'm hoping someone in the community might have already dealt with something of this sort.

I'm trying to create an altcdfenv (or analogous package) remapping the probes from a custom chip onto new gene sequences.  I've read the excellent vignette, matched the probes, made the cdfenv and all seemed well, but:

mas5(Data)
background correction: mas 
PM/MM correction : mas 
expression values: mas 
background correcting...Error in as.vector(data) : NA/NaN/Inf in foreign function call (arg 1)

I looked deeper and found that this is because, as I might have realized, all the MM probes are set to NA by buildCdfEnv, although it happily opens the original cdf where the locations of all the pm/mm pairs are identified.  Here's one probe set in the alt.cdf:

             mm
 [1,] 219922 NA
 [2,] 255744 NA
 [3,] 313097 NA
 [4,] 378979 NA
 [5,] 214348 NA
 [6,] 279991 NA
 [7,] 228789 NA
 [8,] 503799 NA
 [9,]  78517 NA
[10,] 253259 NA
[11,] 367820 NA
[12,] 407971 NA
[13,] 280585 NA
[14,]  68092 NA

Not being very good at R, how hard would it be to recover the mm probes that correspond to these guys?  I'd appreciate any advice.

Thanks,
Mike




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